Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain.
Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.
Nat Commun. 2024 Jan 16;15(1):544. doi: 10.1038/s41467-023-44622-z.
What a strain is and how many strains make up a natural bacterial population remain elusive concepts despite their apparent importance for assessing the role of intra-population diversity in disease emergence or response to environmental perturbations. To advance these concepts, we sequenced 138 randomly selected Salinibacter ruber isolates from two solar salterns and assessed these genomes against companion short-read metagenomes from the same samples. The distribution of genome-aggregate average nucleotide identity (ANI) values among these isolates revealed a bimodal distribution, with four-fold lower occurrence of values between 99.2% and 99.8% relative to ANI >99.8% or <99.2%, revealing a natural "gap" in the sequence space within species. Accordingly, we used this ANI gap to define genomovars and a higher ANI value of >99.99% and shared gene-content >99.0% to define strains. Using these thresholds and extrapolating from how many metagenomic reads each genomovar uniquely recruited, we estimated that -although our 138 isolates represented about 80% of the Sal. ruber population- the total population in one saltern pond is composed of 5,500 to 11,000 genomovars, the great majority of which appear to be rare in-situ. These data also revealed that the most frequently recovered isolate in lab media was often not the most abundant genomovar in-situ, suggesting that cultivation biases are significant, even in cases that cultivation procedures are thought to be robust. The methodology and ANI thresholds outlined here should represent a useful guide for future microdiversity surveys of additional microbial species.
尽管种群内多样性在疾病出现或对环境干扰的反应中的作用十分明显，但什么是菌株以及有多少菌株构成一个自然细菌种群仍然是难以捉摸的概念。为了推进这些概念，我们对来自两个盐田的 138 个随机选择的盐红菌（Salinibacter ruber）分离株进行了测序，并将这些基因组与来自相同样本的伴随短读宏基因组进行了比较。这些分离株的基因组平均核苷酸同一性（ANI）值的分布呈现双峰分布，ANI 值在 99.2%至 99.8%之间的情况比 ANI 值>99.8%或<99.2%的情况出现的频率低四倍，这表明在种内的序列空间存在自然“间隙”。因此，我们使用这个 ANI 间隙来定义基因组变种，使用>99.99%的更高 ANI 值和>99.0%的共享基因含量来定义菌株。使用这些阈值，并根据每个基因组变种独特招募的宏基因组读数的数量进行推断，我们估计 -尽管我们的 138 个分离株代表了大约 80%的盐红菌种群 - 一个盐田池塘中的总种群由 5500 到 11000 个基因组变种组成，其中绝大多数似乎在原位很少见。这些数据还表明，在实验室培养基中最常回收的分离株通常不是原位最丰富的基因组变种，这表明即使培养程序被认为是稳健的，培养偏差也很显著。这里概述的方法和 ANI 阈值应该代表对其他微生物物种进行额外微观多样性调查的有用指南。
